def test_two_aa_pdb(self):
self.o.read_pdb(DataPath + '2AAD.pdb')
frame = 0
phi = 0.0
theta = numpy.pi / 2.0
psi = 0.0
#
self.o.rotate_euler(frame, phi, theta, psi)
result_coor = self.o.coor()
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_coor:\n'
util.printfl([result_coor])
print '\nresult_com:\n', util.printfl([result_com])
#
expected_coor = numpy.array(
[[[41.652, 41.799, -73.944], [40.456, 42.563, -74.229],
[40.463, 43.093, -75.667], [39.401, 43.279, -76.264],
[40.336, 43.734, -73.210], [39.926, 43.168, -71.856],
[39.354, 44.782, -73.67], [39.946, 44.177, -70.721],
[41.647, 43.330, -76.231], [41.730, 43.852, -77.592],
[42.184, 42.820, -78.617], [42.656, 43.169, -79.712],
[42.648, 45.097, -77.671], [43.910, 44.816, -77.054],
[42.000, 46.273, -76.970]]], floattype)
expected_com = numpy.array([41.276, 43.708, -75.680], floattype)
self.assert_list_almost_equal(expected_coor, result_coor, 1)
self.assert_list_almost_equal(expected_com, result_com, 2)
def test_one_atom_pdb_norotate(self):
self.o.read_pdb(DataPath+'1ATM.pdb')
frame = 0
theta=0.0
#
self.o.rotate_general_axis(frame,theta,[0.2,1.3,-3.5])
result_coor = self.o.coor()
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_coor:\n'; util.printfl([result_coor]); print '\nresult_com:\n',util.printfl([result_com])
#
expected_coor = numpy.array([[[73.944, 41.799, 41.652]]], floattype)
expected_com = numpy.array([73.944, 41.799, 41.652], floattype)
self.assert_list_almost_equal(expected_coor, result_coor,3)
self.assert_list_almost_equal(expected_com, result_com,3)
def test_one_atom_pdb(self):
self.o.read_pdb(DataPath+'1ATM.pdb')
axis = 'x'
frame = 0
theta=numpy.pi/2.0
#
self.o.rotate_general_axis(frame,theta,[0.2,1.3,-3.5])
result_coor = self.o.coor()
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_coor:\n'; util.printfl([result_coor]); print '\nresult_com:\n',util.printfl([result_com])
#
expected_coor = numpy.array([[[-215.775, 167.484, 356.058]]], floattype)
expected_com = numpy.array([-215.775, 167.484, 356.058], floattype)
self.assert_list_almost_equal(expected_coor, result_coor,3)
self.assert_list_almost_equal(expected_com, result_com,3)
def test_one_atom_pdb(self):
self.o.read_pdb(DataPath+'1ATM.pdb')
axis = 'x'
frame = 0
theta=numpy.pi/2.0
#
self.o.rotate(frame,axis,theta)
result_coor = self.o.coor()
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_coor:\n'; util.printfl([result_coor]); print '\nresult_com:\n',util.printfl([result_com])
#
expected_coor = numpy.array([[[73.944, -41.652, 41.799]]], floattype)
expected_com = numpy.array([73.944, -41.652, 41.799], floattype)
self.assert_list_almost_equal(expected_coor, result_coor,3)
self.assert_list_almost_equal(expected_com, result_com,3)
def test_two_aa_pdb(self):
self.o.read_pdb(DataPath+'2AAD.pdb')
axis = 'y'
frame = 0
theta=numpy.pi/2.0
#
self.o.rotate(frame,axis,theta)
result_coor = self.o.coor()
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_coor:\n'; util.printfl([result_coor]); print '\nresult_com:\n',util.printfl([result_com])
#
expected_coor = numpy.array([[[41.652, 41.799, -73.944], [40.456, 42.563, -74.229], [40.463, 43.093, -75.667], [39.401, 43.279, -76.264], [40.336, 43.734, -73.210], [39.926, 43.168, -71.856], [39.354, 44.782, -73.67], [39.946, 44.177, -70.721], [41.647, 43.330, -76.231], [41.730, 43.852, -77.592], [42.184, 42.820, -78.617], [42.656, 43.169, -79.712], [42.648, 45.097, -77.671], [43.910, 44.816, -77.054], [42.000, 46.273, -76.970]]], floattype)
expected_com = numpy.array([41.276, 43.708, -75.680], floattype)
self.assert_list_almost_equal(expected_coor, result_coor,1)
self.assert_list_almost_equal(expected_com, result_com,2)
def test_one_atom_pdb(self):
self.o.read_pdb(DataPath + '1ATM.pdb')
axis = 'x'
frame = 0
theta = numpy.pi / 2.0
#
self.o.rotate(frame, axis, theta)
result_coor = self.o.coor()
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_coor:\n'
util.printfl([result_coor])
print '\nresult_com:\n', util.printfl([result_com])
#
expected_coor = numpy.array([[[73.944, -41.652, 41.799]]], floattype)
expected_com = numpy.array([73.944, -41.652, 41.799], floattype)
self.assert_list_almost_equal(expected_coor, result_coor, 3)
self.assert_list_almost_equal(expected_com, result_com, 3)
def test_one_atom_pdb_norotate(self):
self.o.read_pdb(DataPath + '1ATM.pdb')
frame = 0
phi = 0.0
theta = 0.0
psi = 0.0
#
self.o.rotate_euler(frame, phi, theta, psi)
result_coor = self.o.coor()
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_coor:\n'
util.printfl([result_coor])
print '\nresult_com:\n', util.printfl([result_com])
#
expected_coor = numpy.array([[[73.944, 41.799, 41.652]]], floattype)
expected_com = numpy.array([73.944, 41.799, 41.652], floattype)
self.assert_list_almost_equal(expected_coor, result_coor, 3)
self.assert_list_almost_equal(expected_com, result_com, 3)
def test_rna_pdb(self):
self.o.read_pdb(DataPath+'rna.pdb')
frame = 0
theta=numpy.pi/3.0
#
self.o.rotate_general_axis(frame,theta,[0.2,1.3,-3.5])
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_com:\n',util.printfl([result_com])
#
expected_com = numpy.array([-30.425, -38.942, 44.267], floattype)
self.assert_list_almost_equal(expected_com, result_com,2)
def test_two_aa_pdb(self):
self.o.read_pdb(DataPath+'2AAD.pdb')
frame = 0
theta=numpy.pi/2.0
#
self.o.rotate_general_axis(frame,theta,[0.2,1.3,-3.5])
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_com:\n',util.printfl([result_com])
#
expected_com = numpy.array([-221.139, 178.873, 343.429], floattype)
self.assert_list_almost_equal(expected_com, result_com,2)
def test_1CRN_pdb(self):
self.o.read_pdb(DataPath+'1CRN.pdb')
frame = 0
theta=numpy.pi/2.0
#
self.o.rotate_general_axis(frame,theta,[0,1,0])
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_com:\n',util.printfl([result_com])
#
expected_com = numpy.array([-6.978, 9.775, 9.300], floattype)
self.assert_list_almost_equal(expected_com, result_com,2)
def test_1CRN_pdb(self):
self.o.read_pdb(DataPath + '1CRN.pdb')
frame = 0
theta = numpy.pi / 2.0
#
self.o.rotate_euler(frame, theta, theta, theta)
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_com:\n', util.printfl([result_com])
#
expected_com = numpy.array([6.978, -9.775, 9.300], floattype)
self.assert_list_almost_equal(expected_com, result_com, 2)
def test_1KP8_pdb(self):
self.o.read_pdb(DataPath+'1KP8.pdb')
frame = 0
theta=12.0
#
self.o.rotate_general_axis(frame,theta,[0,1,0])
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_com:\n',util.printfl([result_com])
#
expected_com = numpy.array([84.358, 0.251, -22.552], floattype)
self.assert_list_almost_equal(expected_com, result_com,2)
def test_rna_pdb(self):
self.o.read_pdb(DataPath + 'rna.pdb')
axis = 'z'
frame = 0
theta = numpy.pi / 2.0
#
self.o.rotate(frame, axis, theta)
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_com:\n', util.printfl([result_com])
#
expected_com = numpy.array([-4.352, -8.033, 9.231], floattype)
self.assert_list_almost_equal(expected_com, result_com, 2)
def test_1KP8_pdb(self):
self.o.read_pdb(DataPath+'1KP8.pdb')
axis = 'x'
frame = 0
theta=12.0
#
self.o.rotate(frame,axis,theta)
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_com:\n',util.printfl([result_com])
#
expected_com = numpy.array([83.286, 14.288, 22.003], floattype)
self.assert_list_almost_equal(expected_com, result_com,2)
def test_rna_pdb(self):
self.o.read_pdb(DataPath+'rna.pdb')
axis = 'z'
frame = 0
theta=numpy.pi/2.0
#
self.o.rotate(frame,axis,theta)
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_com:\n',util.printfl([result_com])
#
expected_com = numpy.array([-4.352, -8.033, 9.231], floattype)
self.assert_list_almost_equal(expected_com, result_com,2)
def test_1KP8_pdb(self):
self.o.read_pdb(DataPath + '1KP8.pdb')
axis = 'x'
frame = 0
theta = 12.0
#
self.o.rotate(frame, axis, theta)
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_com:\n', util.printfl([result_com])
#
expected_com = numpy.array([83.286, 14.288, 22.003], floattype)
self.assert_list_almost_equal(expected_com, result_com, 2)
def test_1KP8_pdb(self):
self.o.read_pdb(DataPath+'1KP8.pdb')
frame = 0
phi=0.3
theta=2.0
psi=2.3
#
self.o.rotate_euler(frame,phi,theta,psi)
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_com:\n',util.printfl([result_com])
#
expected_com = numpy.array([47.025, 47.438, 56.242], floattype)
self.assert_list_almost_equal(expected_com, result_com,2)
def test_1KP8_pdb(self):
self.o.read_pdb(DataPath + '1KP8.pdb')
frame = 0
phi = 0.3
theta = 2.0
psi = 2.3
#
self.o.rotate_euler(frame, phi, theta, psi)
result_com = self.o.calculate_center_of_mass(0)
print '\nresult_com:\n', util.printfl([result_com])
#
expected_com = numpy.array([47.025, 47.438, 56.242], floattype)
self.assert_list_almost_equal(expected_com, result_com, 2)